OBJECTIVES:  The inclusion of conjugate pneumococcal vaccines to the Regional Immunization Program avoids cases, among others, of invasive pneumococcal diseases caused by serotypes of  Streptococcus pneumoniae contained in the vaccines. Research objective was to assess efficiency of conjugate pneumococcal vaccine- 13 valent (PCV13) versus 10 valent (PCV10), under National Health System perspective. METHODS:  A cost-utility model was developed to estimate cost per quality adjusted life year (QALY) associated to primary bacteriemic, empyema, meningitis and bacteriemic pneumonia with vaccine administration in the Autonomous Region of Madrid.  The estimation of cases to avoid and serotype coverage was based on epidemiologic information available at regional level. Additionally to direct protection, the model considers the potential indirect effect on the general population. One-way sensitivity analyses were performed, including parameters with most uncertainty. RESULTS:  PCV13 yields 224 QALYs versus 70 QALYs with PCV10. The incremental ratio is €16,908/QALY gained. Deterministic sensitivity analysis showed that model results are robust, parameter that most influence on the results was vaccine indirect effect. Reducing PCV13 vaccine schedule from 4 to 3 doses was a dominant strategy. CONCLUSIONS: The inclusion of PCV13 is a cost-effective strategy versus PCV10. A 3 doses schedule of PCV13 is a dominant option, being a cost-saving measure for the National Healthcare System.